Harvard University investment managers had another good year in 2012, while Harvard president Drew Gilpin Faust topped the $1 million mark in total compensation for the first time, the university disclosed Friday.

Harvard Management chief Jane Mendillo received $4.8 million that year, down from $5.3 million in 2011, while five of her managers received $4 million or more as the stock market continued its upward march, helping to boost the value of the endowment they manage.

Andy Wiltshire, who handles alternative investments such as hedge funds and private equity, was the highest paid endowment manager for at least the third year in a row. He made $7.9 million in total compensation, while Alvaro Aguirre-Simunovic, who manages a portfolio of natural resources, earned $6.6 million.

The large payouts are more common on Wall Street than academia, but that is because Harvard Management Co. operates as an investment firm overseeing the Cambridge school’s massive $32.7 billion endowment, the largest of any college. Harvard officials estimate the university saved $1 billion by largely managing the investments in house and say the payments are largely based on the performance of the school’s investments.

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The growth in payouts to some of the endowment managers parallels gains in the stock market. The S&P 500, for instance, notched a 13 percent gain in 2012, its best performance in three years. And while Harvard’s investment gains were flat in the fiscal year ending in June 2012, it grew 11 percent in the year ended in June 2013.

“We are fortunate to have exceptional talent that delivers market-beating performance,” said James F. Rothenberg, Harvard’s treasurer and chairman of the management company’s board.

Faust, who became president in 2007, earned just over $1 million in total compensation in 2012, including nearly $138,000 in nontaxable benefits for the value of her housing in Cambridge and other perks. That is up from $899,734 in calendar year 2011, a 16 percent rise. Separately, the Civil War historian also received another $250,000 in cash and stock for her service on the board of Staples Inc., the Framingham office supply chain.

Faust, 66, joins a growing group of private college presidents to surpass the $1 million mark as university leaders are increasingly paid like executives running large companies. Overall, at least 42 college leaders earned $1 million a year in 2011, according to a survey by the Chronicle of Higher Education, a development that colleges defend but has troubled watchdog groups worried about the rising cost of education.

Alan Garber, the school’s provost, earned nearly $751,000 in 2012, including $100,000 in housing and other nontaxable benefits. Two professors approached or surpassed the $1 million mark because of one-time payments. Economist Amartya K. Sen received $1.2 million (including a payment as part of Sen’s recruitment package), while emeritus business school professor Roy D. Shapiro received $979,000, including a $721,000 retirement payment.